Chapter 2: The Chemistry of Life – Study Notes for Anatomy & Physiology

Chapter 2: The Chemistry of Life

Introduction

This chapter introduces the foundational chemical principles essential for understanding human anatomy and physiology. It covers the structure of matter, the role of elements and compounds in the body, and the chemical properties of water, acids, bases, salts, and major organic molecules.

Atoms and Elements

Definition and States of Matter

• Matter is anything that has mass and occupies space. It exists in three states: solid, liquid, and gas.

• The study of matter and its interactions is called chemistry.

• An element is the simplest form of matter that retains its unique properties.

• Elements are made up of atoms, which consist of subatomic particles: protons (positive charge), neutrons (neutral), and electrons (negative charge).

Major Elements in the Human Body

• The human body is primarily composed of four major elements: Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N).

• There are also several trace elements essential for physiological processes, including Na (sodium), K (potassium), Cl (chloride), Mg (magnesium), Ca (calcium), PO4 (phosphate), and S (sulfur).

• Hydrogen atom is often referred to as a proton (H+) in biological contexts.

Inorganic Compounds

Definition and Types

• Inorganic compounds generally do not contain carbon-hydrogen (C-H) bonds. Examples include water (H2O), acids, bases, and salts.

• Organic compounds contain carbon atoms bonded to hydrogen and often form the basis of living organisms.

Water

Importance and Functions

• Water makes up 50–65% of the human body mass.

• It serves as a medium for metabolic reactions and transports chemicals throughout the body.

• Water helps regulate and transport heat, cushions and protects body structures, and acts as a lubricant between adjacent surfaces (e.g., joints).

Properties of Water

• Water is the body's primary solvent, dissolving many substances necessary for life.

• Hydrophilic substances are "water-loving" and dissolve easily in water (e.g., ions, polar molecules).

• Hydrophobic substances are "water-fearing" and do not dissolve well in water (e.g., nonpolar molecules).

• Water is a polar covalent molecule, with a partial negative charge (δ-) near the oxygen atom and partial positive charges (δ+) near the hydrogen atoms.

Solubility Terms

• Ionic molecules: Very soluble in water.

• Polar molecules: Very soluble in water.

• Nonpolar molecules: Poorly or not soluble in water.

• Amphipathic molecules: Have both hydrophilic and hydrophobic regions; hydrophilic regions interact with water, hydrophobic regions cluster together.

Acids, Bases, and Salts

Acids and Bases

• Acids are substances that donate hydrogen ions (protons, H+) in solution. Example: $\mathrm{HCl} \rightarrow \mathrm{H}^+ + \mathrm{Cl}^-$

• Bases are substances that accept hydrogen ions or release hydroxide ions (OH-).

• The pH scale measures hydrogen ion concentration: pH 7 is neutral, below 7 is acidic, above 7 is basic (alkaline).

• Buffers are chemical systems that resist changes in pH when acids or bases are added.

Salts and Electrolytes

• Salts dissolve in water to form cations (positively charged ions) and anions (negatively charged ions).

• These ions are called electrolytes and are essential for conducting electrical currents in the body.

Table: Important Ions in the Human Body

Ion	Symbol	Significance
Calcium	Ca2+	Part of bones and teeth; blood clotting; muscle contraction; neurotransmitter release
Sodium	Na+	Membrane potentials; water balance
Potassium	K+	Membrane potentials
Hydrogen	H+	Acid-base balance
Hydroxide	OH-	Acid-base balance
Chloride	Cl-	Water balance
Bicarbonate	HCO3-	Acid-base balance
Ammonium	NH4+	Acid-base balance
Phosphate	PO43-	Part of bones and teeth; energy exchange; acid-base balance
Iron	Fe	Red blood cell function
Magnesium	Mg2+	Necessary for enzyme function

Organic Compounds

Monomers and Polymers

• Organic compounds include carbohydrates, lipids, proteins, and nucleic acids.

• Monomers are small subunits that can be combined to form larger molecules called polymers.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen (CHO).

• Serve as fuel and have structural roles.

• Monosaccharides are the simplest carbohydrates (e.g., glucose, fructose, galactose, ribose).

• Disaccharides are formed by joining two monosaccharides (e.g., sucrose, lactose).

• Polysaccharides are long chains of monosaccharides (e.g., glycogen, the storage form of glucose in animals).

Lipids

• Hydrophobic molecules including fats, oils, and steroids; low solubility in water.

• Fatty acids are lipid monomers; can be saturated (no double bonds, solid at room temperature) or unsaturated (one or more double bonds, liquid at room temperature).

• Triglycerides consist of three fatty acids linked to a glycerol backbone; primary energy storage lipid.

• Phospholipids have a glycerol backbone, two fatty acid tails, and a phosphate group; major component of cell membranes.

• Steroids have a characteristic four-ring hydrocarbon structure (e.g., cholesterol, sex hormones).

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.

• Made from 20 different amino acids linked by peptide bonds.

• Functions include: structure, movement, transport, defense (antibodies), catalysis (enzymes), and as fuel.

• Protein structure has four levels: primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D folding), and quaternary (multiple polypeptide chains).

• Denaturation is the loss of protein structure due to changes in temperature, pH, or chemicals, resulting in loss of function.

Enzymes

• Enzymes are proteins that catalyze (speed up) chemical reactions by lowering the activation energy required.

• Enzyme deficiencies can lead to diseases (e.g., Tay-Sachs, SCIDs, PKU).

• Enzyme activity is crucial for metabolism and homeostasis.

Nucleic Acids

• Composed of monomers called nucleotides, each containing a nitrogenous base, a sugar (ribose or deoxyribose), and a phosphate group.

• DNA (deoxyribonucleic acid) is double-stranded, stores genetic information, and contains the bases adenine (A), guanine (G), cytosine (C), and thymine (T).

• RNA (ribonucleic acid) is single-stranded, involved in protein synthesis, and contains uracil (U) instead of thymine.

• ATP (adenosine triphosphate) is the primary energy carrier in cells, produced from ADP and inorganic phosphate using energy from fuel oxidation.

Key Equations

• ATP formation: $\mathrm{ADP} + \mathrm{P}_i + \text{energy} \rightarrow \mathrm{ATP}$

• ATP hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

Concept Check

• The building blocks of proteins are amino acids.

• Monosaccharides are the building blocks of carbohydrates.

• A nucleotide is composed of a sugar, phosphate group, and nitrogenous base.

• The double-stranded polynucleotide is DNA.